Organisms and Ecosystems Review

D3.1 Reproduction

• Reproduction Overview: Reproduction is the production of offspring by parents. It is categorized into two main types:     * Sexual Reproduction: Involves two parents ($+$-sign indicating different types). It requires meiosis in every life cycle, produces offspring that are genetically different from each other and their parents, and generates genetic variation through new gene combinations. Advantage: allows species to evolve in changing environments as offspring may be better adapted than parents.     * Asexual Reproduction: Involves one parent. It relies on mitosis only (no meiosis). Offspring are genetically identical to each other and the parent (clones). No genetic variation is generated in existing gene combinations. Advantage: in an unchanging environment, well-adapted parents produce offspring that are also well-adapted.

• Roles in Sexual Reproduction:     * Fusion of Gametes (Fertilization): Male and female gametes join to form a new individual. This brings different alleles (gene versions) together in new combinations. Fertilization doubles the chromosome number in each occurrence.     * Meiosis: A diploid nucleus divides to form four haploid nuclei, halving the chromosome number. This process breaks up parental gene combinations, allowing new ones to form during fusion. It reverses the doubling caused by fertilization to maintain a stable chromosome number across generations.

• Comparison of Male and Female Gametes:     * Motility: Male gametes travel to the female; female gametes are non-motile.     * Size: Male gametes are smaller for faster movement; female gametes are larger due to food reserve stores.     * Food Reserves: Male gametes have minimal reserves (only for the gamete); female gametes have more to support embryo development.     * Numbers: Male gametes are produced in very large numbers; female gametes are produced in few numbers (sometimes only one).

• Male Reproductive System Structures:     * Testis: Produces sperm and testosterone.     * Epididymis: Stores sperm until ejaculation.     * Scrotum: Holds testes at lower than core body temperature to promote sperm development.     * Sperm Duct: Transfers sperm during ejaculation.     * Seminal Vesicles & Prostate Gland: Secrete fluid containing alkali, proteins, and fructose to make semen.     * Urethra: Transfers semen during ejaculation and urine during urination.     * Penis: Penetrates the vagina for ejaculation near the cervix; contains erectile tissue that fills with blood.

• Female Reproductive System Structures:     * Ovary: Produces eggs, oestradiol, and progesterone.     * Oviduct: Collects eggs during ovulation, provides the site for fertilization, and moves the embryo to the uterus.     * Uterus: Provides for the needs of the embryo and foetus (protection, food/oxygen supply, waste removal).     * Cervix: Protects the foetus and dilates to provide a birth canal.     * Vagina: Stimulates the penis for ejaculation and acts as the birth canal.     * Vulva: Protects internal reproductive parts.

• The Menstrual Cycle (Hormonal Control):     * The cycle lasts roughly $28$ days. Day $1$ is defined by the start of menstruation.     * Ovarian Cycle: Follicles develop in the ovary; usually, one releases an egg (ovulation) around Day $14$. The empty follicle becomes the corpus luteum, which breaks down if no embryo is present.     * Uterine Cycle: The endometrium (inner layer) thickens in preparation for implantation. If no embryo is present, it breaks down and passes out (menstruation).     * FSH (Follicle-stimulating hormone): Produced by the pituitary. Rises in the first $10$ days. Stimulates follicle development and oestradiol secretion.     * LH (Luteinizing hormone): Produced by the pituitary. Peaks sharply around Day $14$. Stimulates oocyte maturation, ovulation, and corpus luteum development.     * Oestradiol: Produced by follicle walls. Peaks in the second week. Stimulates endometrium repair/thickening. High levels inhibit FSH (negative feedback) and stimulate LH (positive feedback).     * Progesterone: Produced by the corpus luteum. Levels peak after ovulation. Promotes and maintains the endometrium. Inhibits FSH and LH (negative feedback).

• Fertilization and Early Development:     * Sperm detect chemicals from the egg to swim toward it. The egg is surrounded by follicle cells and the glycoprotein layer (zona pellucida).     * Sperm digest a route through glycoproteins; proteins on the sperm’s membrane bind to the egg’s membrane, and the nuclei fuse.     * The zona pellucida hardens immediately after the first sperm entry to prevent polyspermy.     * Sperm mitochondria are destroyed by the egg; the sperm tail is either left outside or broken down.     * The nuclei remain separate until the first mitosis, where they release $23$ chromosomes each to form a single spindle. The resulting nuclei (46 chromosomes) are genetically identical.

• In Vitro Fertilization (IVF):     1. Down-regulation: Drugs (nasal spray/injection) for $2$ weeks stop pituitary secretion of FSH/LH to pause the cycle.     2. FSH injections: Given daily for $7$–$12$ days to stimulate superovulation ($8$–$15$ follicles).     3. hCG injection: Administered when follicles reach $18\,mm$ to stimulate maturation.     4. Egg collection: Micropipette used via ultrasound scanning approximately $36$ hours after hCG.     5. Fertilization: Eggs mixed with $50,000$–$100,000$ sperm in a dish at $37\,°C$.     6. Embryo transfer: Embryos ($48$ hours old) placed in the uterus; progesterone is given to maintain the lining.

• Sexual Reproduction in Flowering Plants:     * Stamen (Male): Consists of the anther (produces pollen via meiosis/mitosis) and filament.     * Carpel (Female): Consists of the stigma (receives pollen), style (pollen tube growth), and ovary (contains ovules).     * Meiosis: Occurs in anthers to produce haploid pollen and in ovules to produce the egg nucleus.     * Pollination: Transfer of pollen from anther to stigma via wind or animals.     * Fertilization: Pollen tube grows down the style to the ovary/ovule. The male gamete is released to fuse with the egg nucleus to form a zygote.     * Embryo Development: Zygote divides via mitosis to form an embryo root, shoot, and cotyledon(s); ovule layers become the seed coat.

• Pollination Strategies:     * Insect-pollinated flowers: Feature large, brightly colored petals, scent, nectar (protein-rich pollen/sugar-rich nectar), and spiky pollen grains. Nectaries are positioned deep to ensure contact with anthers/stigma.     * Cross-pollination: Transfer of pollen to a different plant. Promotes genetic variation/evolution and reduces inbreeding.     * Self-pollination: Transfer within the same plant; can lead to inbreeding and expression of recessive genetic disorders. Offspring of different plants show hybrid vigour.     * Mechanisms to increase cross-pollination: Separate male/female plants (Ginkgo biloba), separate flowers on the same plant (Zea mays), or different maturation times (protandry - pollen first; protogyny - stigma first).     * Self-incompatibility: A genetic mechanism where pollen fails to germinate or grow on the stigma of the same plant (e.g., Apple trees with different $S$-alleles).

• Seed Dispersal and Germination:     * Dispersal methods: Fleshy/attractive (animals), feathery/winged (wind), hooks (animal coats), or explosive (Cranesbill).     * Germination conditions: Requires water, oxygen, and warmth.

D3.2 Inheritance

• Basics of Inheritance:     * Diploid body cells have two copies of each autosomal gene. Gametes are haploid (one copy). Fusion restores the diploid number ($46$ in humans).     * Genotype: The combination of alleles (e.g., $DD$, $Dd$, $dd$).     * Phenotype: Observable traits (structural or functional). Influenced by genotype, environment, or both.         * Genotype only: Eye color, haemophilia, ability to smell $\beta$-ionone.         * Environment only: Scars, river blindness, tattoos.         * Both: Height, autism, diabetes.

• Mendelian Inheritance:     * Dominant Alleles: Determine phenotype in both homozygous ($SS$) and heterozygous ($Ss$) states.     * Recessive Alleles: Determine phenotype only in homozygous recessive ($ss$) individuals.     * Mendel's Law of Segregation: The two alleles of each gene separate into different haploid daughter nuclei during meiosis.     * Starch-Branching Enzyme (SBE1): Smooth seeds ($S$) have functional enzymes; wrinkled seeds ($s$) have non-functional versions leading to sugar buildup.

• Phenotypic Plasticity: Reversible form of adaptation where environmental changes (e.g., sunlight) switch gene expression on or off (e.g., melanin production) without changing the underlying alleles.

• Genetic Diseases and Genes:     * Phenylketonuria (PKU): Recessive disorder caused by a lack of phenylalanine hydroxylase. Excess phenylalanine impairs brain development. Prevented by birth screening and low-phenylalanine diets.     * Gene Pools: All genes in a breeding population. Evolution is change in the gene pool over time.     * SNPs (Single Nucleotide Polymorphisms): Positions in a gene where different bases can be present. Multiple alleles (e.g., over $30$ $S$-alleles in apples) arise from these variants.     * ABO Blood Groups: Controlled by alleles $I^A$, $I^B$ (codominant), and $i$ (recessive).         * Group A: $I^A I^A$ or $I^A i$.         * Group B: $I^B I^B$ or $I^B i$.         * Group AB: $I^A I^B$.         * Group O: $ii$.     * Codominance vs. Incomplete Dominance:         * Codominance: Dual phenotype (e.g., Blood group AB antigens).         * Incomplete Dominance: Intermediate phenotype (e.g., Pink flowers from Red $C^R C^R$ and White $C^W C^W$ Mirabilis jalapa).

• Sex Chromosomes and Linkage:     * Determined by the $23$rd pair: females $XX$, males $XY$.     * TDF (Testis-Determining Factor): Gene on the $Y$ chromosome that triggers male development.     * Haemophilia: Sex-linked recessive disorder on the $X$ chromosome (Factor VIII deficiency). Frequent in males ($X^h Y$) as they have only one $X$; females are usually carriers ($X^H X^h$).

• Pedigree Charts and Statistical Skills:     * Used to deduce inheritance patterns. Squares/circles represent males/females. Affected individuals are shaded.     * Polygenic Inheritance: Traits like skin color determined by multiple genes, resulting in continuous variation.     * Measures of Central Tendency: Mean (average), Median (middle value), Mode (most common). The normal distribution shows these values near each other.     * Box-and-Whisker Plots: Represent variability and range. Includes median, quartiles (IQR), and outliers (> 1.5 \times \text{IQR} from quartiles).

D3.3 Homeostasis

• The Internal Environment: Homeostasis keeps variables (blood glucose, osmotic concentration, pH, and core temperature) near optimal levels despite external fluctuations. This occurs in tissue fluid between cells.

• Negative Feedback: The basis of homeostasis. It decreases the gap between the original level and a set-point to restore balance. In contrast, positive feedback promotes change/instability.

• Regulation of Blood Glucose:     * High Levels: $\beta$ cells in the pancreas secrete insulin. Stimulates liver/muscles to convert glucose to glycogen; other cells use glucose for respiration. This lowers blood glucose.     * Low Levels: $\alpha$ cells in the pancreas secrete glucagon. Stimulates liver cells to break down glycogen into glucose. This raises blood glucose.     * Normal limits: $4$ to $8$ millimoles per litre.

• Diabetes Mellitus:     * Type 1: Immune system destroys $\beta$ cells. Requires insulin injections. Onset in youth.     * Type 2: Target cells become insulin-insensitive (receptor deficiency). Often linked to obesity/diet. Treated with diet, exercise, and weight loss.

• Thermoregulation:     * Integrating centre: Hypothalamus. Monitors peripheral (skin) and central (core/hypothalamus) thermoreceptors.     * Thyroxin: Hub for metabolic rate control. Secretion increases to raise heat generation.     * Responses to Cold:         * Vasoconstriction: Skin arterioles narrow; less blood to skin reduces heat loss.         * Shivering: Involuntary muscle contractions generate heat.         * Uncoupled Respiration: Brown adipose tissue mitochondria oxidize fat to generate only heat (no ATP).         * Hair Erection: Ineffective in humans (goosebumps); traps air in thicker coats of other mammals.     * Responses to Heat:         * Vasodilation: Skin arterioles widen; increased blood flow to skin promotes heat loss.         * Sweating: Glands secrete sweat; evaporation uses high latent heat of vaporization to cool skin.         * Behavioural: Seeking shade, removing clothes, reducing activity.

D4.1 Natural Selection

• Mechanism of Evolution: Theory popularized by Darwin (1859). Steps: overproduction of offspring $\rightarrow$ variation $\rightarrow$ struggle for existence (competition) $\rightarrow$ survival/reproduction of the fittest $\rightarrow$ inheritance of adaptive features.

• Sources of Variation:     1. Mutation: Original source producing new alleles.     2. Meiosis: Crossing over and independent orientation produce new allele combinations.     3. Fertilization: Combines alleles from two different parents.

• Selection Pressures: Factors inducing survival differences. Examples:     * Abiotic: Temperature, nitrogen availability (often density-independent).     * Biotic: Predation, disease (often density-dependent).

• Sexual Selection: Mate choice based on fitness indicators. Example: Birds of Paradise (Astrapia mayeri). Males have long tail feathers and bright plumage; females prefer these despite the survival risk, as they indicate health/vigor.

• Guppy Experiments (John Endler):     * In ponds without predators, male guppies developed more bright spots (sexual selection).     * In ponds with pike-cichlid predators, males became duller to hide (natural selection).     * This demonstrates the rapid evolutionary balance between two opposing selection pressures.

D4.2 Sustainability and Change

• Ecosystem Sustainability: Ecosystems (e.g., Daintree Rainforest) can persist for millions of years if they have: constant energy supply (sunlight), nutrient cycling (replenishing abiotic reserves), stable climate tolerance ranges, and high genetic diversity (especially in keystone species).

• Tipping Points: Sudden environmental changes caused by positive feedback. In the Amazon: Deforestation $\rightarrow$ less transpiration $\rightarrow$ less rain/higher temperature $\rightarrow$ more forest fires/tree death $\rightarrow$ conversion to grassland.

• Mesocosms: Small experimental enclosures (sealed glass vessels/open tanks) used to model ecosystems. Require autotrophs and saprotrophs; consumers are not strictly essential.

• Keystone Species: Have a disproportionate effect on community structure. Example: the sea star Pisaster ochraceus prevents Mytilus (mussel) dominance on rocky shores to maintain biodiversity.

• Harvesting and Human Impact:     * Sustainable harvest requires replacement rate > harvest rate.     * Brazil Nuts: Harvesting from Bertholletia excelsa is only sustainable if some nuts stay for agoutis to bury and germinate.     * Atlantic Cod: Overfishing in the 1990s led to collapse. Sustainability measures (quotas, mesh size, nursery exclusion zones) allowed North Sea biomass to triple since 2005.     * Maximum Sustainable Yield (MSY) is symbolized as point $M$ or $K/2$ on the sigmoid growth curve.

• Agricultural Impacts:     * Soil Degradation: Caused by tillage, erosion, and nutrient depletion.     * Eutrophication: Rainfall leaches nitrate/phosphates into water. Process: $\text{Algal bloom} \rightarrow \text{shading/death} \rightarrow \text{decomposition} \rightarrow \text{high Biochemical Oxygen Demand (BOD)} \rightarrow \text{anaerobic conditions/fish death}$.

• Pollution and Biomagnification:     * Plastic: Macroplastics (>5\,mm), microplastics ($5\,mm$–$1\,\mu m$), nanoplastics (<1\,\mu m). Cause entanglement, gut blockages, and cell-level damage.     * Bioaccumulation: Toxin buildup in an individual's tissues (e.g., methyl mercury in fat).     * Biomagnification: Toxin concentration increases at each successive trophic level (e.g., DDT in ospreys).

• Rewilding: Minimal human intervention to allow natural processes to restore habitats. Example: Hinewai Reserve in New Zealand. Pasture returned to forest via competition; invasive gorse provided a "nurse canopy" for native saplings.

D4.3 Climate Change

• Greenhouse Effect: Gases ($CO_2$, methane) absorb long-wave thermal radiation. Human activities (fossil fuels, deforestation, meat production, rice paddies, landfill gas) enhance this to cause global warming.

• Positive Feedback Cycles:     * Albedo Effect: Ice/snow melt reduces reflection of solar radiation, leading to faster warming.     * Permafrost: Melting leads to anaerobic decomposition of peat, releasing more methane.     * Ocean Solubility: Warmer oceans release dissolved $CO_2$ (reduced solubility).     * Decomposition: High temperatures speed up saprotroph respiration in peatlands.

• Ecosystem Impacts:     * Boreal Forests: Warming turns these carbon sinks into sources as fires release "legacy carbon."     * Ocean Currents: Warming increases stratification (layering), reducing the upwelling of nutrients. El Niño events (becoming more frequent) disrupt productivity in areas like the Galapagos.     * Polar Ice Caps: Loss of landfast/sea ice targets species like Emperor penguins (breeding grounds) and walruses (resting/feeding trips distance).     * Range Shifts: Temperate species shift poleward (North American trees) or upslope on mountains (New Guinea birds shift up to $650\,m$).

• Ocean Acidification and Coral Reefs:     * Industrialization dropped ocean pH from $8.18$ to $8.06$ ($30\%$ acidification).     * Chemistry: $CO_2 + H_2O \rightarrow H_2CO_3 \rightarrow H^+ + HCO_3^-$. Hydrogen ions react with carbonate ($CO_3^{2-}$) to make hydrogencarbonate ($HCO_3^-$). This lowers carbonate availability for coral calcification.     * Coral Bleaching: Warming induces ejection of mutualistic zooxanthellae algae.

• Carbon Sequestration:     * Biological methods include afforestation (planting trees) and wetland restoration (rewetting peatlands by blocking drains and re-establishing Sphagnum moss).